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Merged
labkey-jeckels merged 1 commit into from
May 12, 2026
Merged

Auto-refactor lint cleanup #1130

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10 changes: 2 additions & 8 deletions EHR_App/test/src/org/labkey/test/tests/EHR_AppTest.java
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Expand Up @@ -23,6 +23,7 @@

import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNotEquals;
import static org.junit.Assert.assertTrue;
import static org.labkey.test.components.html.Input.Input;

Expand Down Expand Up @@ -115,12 +116,6 @@ private void doSetup() throws Exception
goToEHRFolder();
}

@Override
public BrowserType bestBrowser()
{
return BrowserType.CHROME;
}

@Override
protected String getModuleDirectory()
{
Expand Down Expand Up @@ -591,8 +586,7 @@ private void assertDemographicsNoRowsHaveStatus(ReactAnimalHistoryPage page, Str
List<String> statusValues = table.getColumnDataAsText("calculated_status");
for (String status : statusValues)
{
assertFalse("Demographics should not contain status '" + excludedStatus + "' but found it",
status.equals(excludedStatus));
assertNotEquals("Demographics should not contain status '" + excludedStatus + "' but found it", status, excludedStatus);
}
}
}
3 changes: 2 additions & 1 deletion EHR_ComplianceDB/src/org/labkey/ehr_compliancedb/model/EHRComplianceDBDomainKind.java
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@@ -1,5 +1,6 @@
package org.labkey.ehr_compliancedb.model;

import org.jetbrains.annotations.NotNull;
import org.labkey.api.data.Container;
import org.labkey.api.exp.property.Domain;
import org.labkey.api.gwt.client.model.GWTPropertyDescriptor;
Expand Down Expand Up @@ -42,7 +43,7 @@ public String getKindName()
}

@Override
public Set<String> getReservedPropertyNames(Domain domain, User user)
public @NotNull Set<String> getReservedPropertyNames(Domain domain, User user)
{
return super.getReservedPropertyNames(domain, user);
}
Expand Down
25 changes: 0 additions & 25 deletions EHR_Purchasing/src/org/labkey/ehr_purchasing/EHR_PurchasingContainerListener.java
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Expand Up @@ -16,7 +16,6 @@

package org.labkey.ehr_purchasing;

import org.jetbrains.annotations.NotNull;
import org.labkey.api.data.Container;
import org.labkey.api.data.ContainerManager.ContainerListener;
import org.labkey.api.data.DbScope;
Expand All @@ -25,16 +24,8 @@
import org.labkey.api.data.TableInfo;
import org.labkey.api.security.User;

import java.beans.PropertyChangeEvent;
import java.util.Collection;
import java.util.Collections;

public class EHR_PurchasingContainerListener implements ContainerListener
{
@Override
public void containerCreated(Container c, User user)
{
}

@Override
public void containerDeleted(Container c, User user)
Expand Down Expand Up @@ -68,20 +59,4 @@ public void containerDeleted(Container c, User user)
transaction.commit();
}
}

@Override
public void propertyChange(PropertyChangeEvent evt)
{
}

@Override
public void containerMoved(Container c, Container oldParent, User user)
{
}

@NotNull @Override
public Collection<String> canMove(Container c, Container newParent, User user)
{
return Collections.emptyList();
}
}
24 changes: 0 additions & 24 deletions EHR_SM/src/org/labkey/ehr_sm/EHR_SMContainerListener.java
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Expand Up @@ -16,42 +16,18 @@

package org.labkey.ehr_sm;

import org.jetbrains.annotations.NotNull;
import org.labkey.api.data.Container;
import org.labkey.api.data.ContainerManager.ContainerListener;
import org.labkey.api.data.PropertyManager;
import org.labkey.api.security.User;
import java.util.Collections;
import java.util.Collection;

import java.beans.PropertyChangeEvent;

public class EHR_SMContainerListener implements ContainerListener
{
@Override
public void containerCreated(Container c, User user)
{
}

@Override
public void containerDeleted(Container c, User user)
{
PropertyManager.purgeObjectProperties(c);
}

@Override
public void propertyChange(PropertyChangeEvent evt)
{
}

@Override
public void containerMoved(Container c, Container oldParent, User user)
{
}

@NotNull @Override
public Collection<String> canMove(Container c, Container newParent, User user)
{
return Collections.emptyList();
}
}
3 changes: 1 addition & 2 deletions EHR_SM/src/org/labkey/ehr_sm/EHR_SMCustomizer.java
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Expand Up @@ -50,7 +50,6 @@ public void customize(TableInfo tableInfo)
if (tableInfo instanceof AbstractTableInfo && props.containsKey(tableInfo.getName()))
{
customizeSamples((AbstractTableInfo) tableInfo);
return;
}
}
}
Expand Down Expand Up @@ -111,7 +110,7 @@ private void customizeSamples(AbstractTableInfo ti)

ColumnInfo receivedCol = ti.getColumn(receivedDateCol);
if (null == receivedCol)
_log.warn("Sample type " + ti.getName() + " does not have column " + receivedDateCol + " for age at sample calculation.");
_log.warn("Sample type {} does not have column {} for age at sample calculation.", ti.getName(), receivedDateCol);

TableInfo demographics = QueryService.get().getUserSchema(ti.getUserSchema().getUser(), ContainerService.get().getForPath(ehrContainerName), "study").getTable("demographics");

Expand Down
7 changes: 0 additions & 7 deletions EHR_SM/src/org/labkey/ehr_sm/EHR_SMModule.java
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Expand Up @@ -17,7 +17,6 @@
package org.labkey.ehr_sm;

import org.jetbrains.annotations.NotNull;
import org.labkey.api.data.Container;
import org.labkey.api.data.ContainerManager;
import org.labkey.api.module.CodeOnlyModule;
import org.labkey.api.module.ModuleContext;
Expand Down Expand Up @@ -56,10 +55,4 @@ public void doStartup(ModuleContext moduleContext)
ContainerManager.addContainerListener(new EHR_SMContainerListener());
}

@Override
@NotNull
public Collection<String> getSummary(Container c)
{
return Collections.emptyList();
}
}
2 changes: 1 addition & 1 deletion Viral_Load_Assay/src/org/labkey/viral_load_assay/ViralLoadCustomizer.java
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Expand Up @@ -60,7 +60,7 @@ private void appendVLCol(AbstractTableInfo ti, ColumnInfo subjectCol, ColumnInfo
List<ExpProtocol> protocols = AssayService.get().getAssayProtocols(target, ap);
if (protocols.size() == 1)
{
AssayProtocolSchema schema = ap.createProtocolSchema(ti.getUserSchema().getUser(), target, protocols.get(0), null);
AssayProtocolSchema schema = ap.createProtocolSchema(ti.getUserSchema().getUser(), target, protocols.getFirst(), null);
if (schema == null)
{
return;
Expand Down
6 changes: 0 additions & 6 deletions Viral_Load_Assay/src/org/labkey/viral_load_assay/Viral_Load_AssayModule.java
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Expand Up @@ -52,12 +52,6 @@ public String getName()
return 12.28;
}

@Override
public boolean hasScripts()
{
return true;
}

@Override
@NotNull
protected Collection<WebPartFactory> createWebPartFactories()
Expand Down
10 changes: 2 additions & 8 deletions Viral_Load_Assay/src/org/labkey/viral_load_assay/assay/ABI7500ImportMethod.java
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Expand Up @@ -385,8 +385,7 @@ protected List<Map<String, Object>> processRowsFromFile(List<Map<String, Object>

if (TYPE.Standard.equals(category))
{
if (map.get("sampleVol") == null)
map.put("sampleVol", 1);
map.putIfAbsent("sampleVol", 1);

if (!(map.get(QUANTITY_FIELD) instanceof Double))
{
Expand All @@ -396,13 +395,8 @@ protected List<Map<String, Object>> processRowsFromFile(List<Map<String, Object>
}
else if (TYPE.NEG_CTL.equals(category))
{
if (map.get("sampleVol") == null)
map.put("sampleVol", 1);
map.putIfAbsent("sampleVol", 1);

if (map.get("cp") != null)
{
map.put("qcflag", "NTC had a value for CT");
}
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@labkey-adam labkey-adam May 12, 2026

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Huh, why is this getting deleted?

}

for (String field : new String[]{"sampleVol", "volPerRxn", "eluateVol"})
Expand Down
4 changes: 1 addition & 3 deletions Viral_Load_Assay/src/org/labkey/viral_load_assay/assay/AbstractWNPRCImportMethod.java
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Expand Up @@ -492,9 +492,7 @@ protected List<Map<String, Object>> processRowsFromFile(List<Map<String, Object>
if (map.get("well") != null) {
map.put("well", ((String) map.get("well")).toUpperCase());
}
if (map.get("sampleType") == null) {
map.put("sampleType", "vRNA");
}
map.putIfAbsent("sampleType", "vRNA");

if (!mergeTemplateRow(keyProperty, templateRows, map, context)) {
continue;
Expand Down
6 changes: 0 additions & 6 deletions Viral_Load_Assay/src/org/labkey/viral_load_assay/assay/DefaultVLImportMethod.java
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Expand Up @@ -49,12 +49,6 @@ public JSONObject getMetadata(ViewContext ctx, ExpProtocol protocol)
return meta;
}

@Override
public boolean supportsRunTemplates()
{
return false;
}

protected enum Category {
STD(){
@Override
Expand Down
3 changes: 2 additions & 1 deletion Viral_Load_Assay/src/org/labkey/viral_load_assay/assay/ViralLoadAssayDataProvider.java
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Expand Up @@ -16,6 +16,7 @@
package org.labkey.viral_load_assay.assay;

import org.json.JSONObject;
import org.jetbrains.annotations.NotNull;
import org.labkey.api.data.Container;
import org.labkey.api.data.ContainerManager;
import org.labkey.api.laboratory.NavItem;
Expand Down Expand Up @@ -119,7 +120,7 @@ public List<NavItem> getSettingsItems(Container c, User u)
}

@Override
public Set<ClientDependency> getClientDependencies()
public @NotNull Set<ClientDependency> getClientDependencies()
{
LinkedHashSet<ClientDependency> resources = new LinkedHashSet<>();
resources.add(ClientDependency.fromPath("Viral_Load_Assay/vl_utils.js"));
Expand Down
9 changes: 1 addition & 8 deletions Viral_Load_Assay/test/src/org/labkey/test/tests/external/labModules/ViralLoadAssayTest.java
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Expand Up @@ -400,7 +400,7 @@ private void ensureABI7500Records() throws CommandException, IOException
else
{
log("ABI7500 already exists, no action needed");
Map<String, Object> row = resp.getRows().get(0);
Map<String, Object> row = resp.getRows().getFirst();
DETECTOR_NAME = (String)row.get("detector");
}
}
Expand Down Expand Up @@ -1050,11 +1050,4 @@ protected List<String> getEnabledModules()
modules.add("Viral_Load_Assay");
return modules;
}

@Override
public void checkViews()
{
//the module contains an R report tied to a specific assay name, so view check fails when an assay of that name isnt present
//when module-based assays can supply reports this should be corrected
}
}
18 changes: 9 additions & 9 deletions ehr/api-src/org/labkey/api/ehr/SharedEHRUpgradeCode.java
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Expand Up @@ -180,7 +180,7 @@ else if (methodName.startsWith(IMPORT_DOMAIN_TEMPLATE))
}
else
{
LOG.error("Domain template '" + domainGroup + "' not found for module '" + moduleName + "'");
LOG.error("Domain template '{}' not found for module '{}'", domainGroup, moduleName);
}
}
}
Expand All @@ -204,18 +204,18 @@ public void moduleStartupComplete(ServletContext servletContext)
Container container = EHRService.get().getEHRStudyContainer(ContainerManager.getRoot());
if (container == null)
{
LOG.warn("No EHR study container. Unable to perform upgrade steps for " + _module.getName());
LOG.warn("No EHR study container. Unable to perform upgrade steps for {}", _module.getName());
return;
}
if (!container.getActiveModules().contains(_module))
{
LOG.warn("EHR container does not have module " + _module.getName() + " enabled. Skipping upgrade work.");
LOG.warn("EHR container does not have module {} enabled. Skipping upgrade work.", _module.getName());
}

User user = EHRService.get().getEHRUser(ContainerManager.getRoot());
if (user == null || !user.isActive())
{
LOG.warn("No EHR admin user. Unable to perform upgrade steps for " + _module.getName());
LOG.warn("No EHR admin user. Unable to perform upgrade steps for {}", _module.getName());
return;
}

Expand All @@ -232,7 +232,7 @@ public void moduleStartupComplete(ServletContext servletContext)
}
else
{
LOG.warn("Unable to find container for path " + tsvImport._containerPath + ". Importing into EHR study container.");
LOG.warn("Unable to find container for path {}. Importing into EHR study container.", tsvImport._containerPath);
importFile(tsvImport, container, user);
}
}
Expand Down Expand Up @@ -260,12 +260,12 @@ public void moduleStartupComplete(ServletContext servletContext)
Pair<Long, String> result = DataIntegrationService.get().truncateTargets(container, user, etlInfo.getKey());
if (result.second != null)
{
LOG.error("Failed to truncate ETL " + etlInfo.getKey() + ", continuing without queuing a run. Details: " + result.second);
LOG.error("Failed to truncate ETL {}, continuing without queuing a run. Details: {}", etlInfo.getKey(), result.second);
continue;
}
if (!DataIntegrationService.get().resetTransformState(container, user, etlInfo.getKey()))
{
LOG.info("No saved state for " + etlInfo.getKey() + " found for reset, starting ETL.");
LOG.info("No saved state for {} found for reset, starting ETL.", etlInfo.getKey());
}
}
}
Expand All @@ -279,7 +279,7 @@ public void moduleStartupComplete(ServletContext servletContext)
}
catch(PipelineJobException | ConfigurationException e)
{
LOG.error("Failed to launch ETL " + etlInfo.getKey(), e);
LOG.error("Failed to launch ETL {}", etlInfo.getKey(), e);
}
}
}
Expand Down Expand Up @@ -311,7 +311,7 @@ private void importFile(TsvImport tsvImport, Container container, User user) thr
throw new IllegalArgumentException("No query update service for " + tsvImport._schemaName + "." + tsvImport._queryName);
}

LOG.info("Importing " + tsvImport._tsvPath + " to " + tsvImport._schemaName + "." + tsvImport._queryName);
LOG.info("Importing {} to {}.{}", tsvImport._tsvPath, tsvImport._schemaName, tsvImport._queryName);

// Delete the current rows
updateService.truncateRows(user, container, null, null);
Expand Down
2 changes: 1 addition & 1 deletion ehr/api-src/org/labkey/api/ehr/buttons/MarkCompletedButton.java
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Expand Up @@ -91,7 +91,7 @@ protected String getJsHandler(TableInfo ti)
String pkColName = null;
if (ti.getPkColumnNames() != null && ti.getPkColumnNames().size() == 1)
{
pkColName = ti.getPkColumnNames().get(0);
pkColName = ti.getPkColumnNames().getFirst();
}

return "EHR.window.MarkCompletedWindow.buttonHandler(dataRegionName, " + PageFlowUtil.jsString(_schemaName) + ", " + PageFlowUtil.jsString(_queryName) + ", " + PageFlowUtil.jsString(xtype) + ", " + PageFlowUtil.jsString(pkColName) + ");";
Expand Down
2 changes: 1 addition & 1 deletion ehr/api-src/org/labkey/api/ehr/dataentry/AbstractFormSection.java
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Expand Up @@ -266,7 +266,7 @@ public Set<TableInfo> getTables(DataEntryFormContext ctx)
TableInfo ti = ctx.getTable(pair.first, pair.second);
if (ti == null)
{
_log.error("Unable to create table: " + pair.first + "." + pair.second);
_log.error("Unable to create table: {}.{}", pair.first, pair.second);
continue;
}

Expand Down
2 changes: 1 addition & 1 deletion ehr/api-src/org/labkey/api/ehr/dataentry/BloodDrawFormSection.java
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Expand Up @@ -48,7 +48,7 @@ public List<String> getTbarMoreActionButtons()
defaultButtons.add("REPEAT_SELECTED");

if (!_isRequest)
defaultButtons.add(0, "ADDBLOODDRAWS");
defaultButtons.addFirst("ADDBLOODDRAWS");

defaultButtons.add("BULK_ADD_BLOOD");

Expand Down
2 changes: 1 addition & 1 deletion ehr/api-src/org/labkey/api/ehr/dataentry/DefaultDataEntryFormFactory.java
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Expand Up @@ -54,7 +54,7 @@ public DataEntryForm createForm(DataEntryFormContext ctx)
}
catch (InstantiationException | IllegalAccessException | InvocationTargetException | NoSuchMethodException e)
{
_log.error("Unable to create form: " + _clazz.getName(), e);
_log.error("Unable to create form: {}", _clazz.getName(), e);
return null;
}
}
Expand Down
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